Genomic characterization of hepaciviruses and pegivirus in the northern tree shrew (Tupaia belangeri)

The northern tree shrew (Tupaia belangeri) is recognized as a valuable animal model for studying hepatitis B and C viruses (HCV). However, natural infections of tree shrews remain to be fully characterized. In this study, we identified tree shrew hepaciviruses 1 and 2 and tree shrew pegivirus in liver samples and determined their complete genome sequences. The sequences of these viruses encoded a single large polyprotein, similar to other Flaviviridae viruses. In the 5′ untranslated region, tree shrew hepaciviruses possesses miR-122 binding sites, which is involved in liver tropism of HCV, whereas tree shrew pegivirus did not. Genetic analysis revealed 58 % amino acid homology between the polyproteins of tree shrew hepaciviruses 1 and 2. Tree shrew hepacivirsues were genetically close to the rodent hepacivirus (Hepacivirus P) detected in long-tailed ground squirrels, and tree shrew pegivirus was close to Pegivirus scotophili detected in bats. Analysis of viral infections revealed that, among the 37 tree shrews tested, 26 were positive for tree shrew hepacivirus 1, of which 15 were also positive for tree shrew hepacivirus 2. Only one tree shrew was positive for the pegivirus. These data indicate that the tree shrews used as experimental animals were infected with various viruses and that viral genomic characterizations are essential for classifying viral species and understanding viral characteristics and evolution. Furthermore, this study will be useful for screening viral infections to establish the tree shrew as a more stable experimental animal.